Starting phenix.real_space_refine on Sat Aug 23 08:21:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e4h_30985/08_2025/7e4h_30985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4h_30985/08_2025/7e4h_30985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e4h_30985/08_2025/7e4h_30985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4h_30985/08_2025/7e4h_30985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e4h_30985/08_2025/7e4h_30985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4h_30985/08_2025/7e4h_30985.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6851 2.51 5 N 1837 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10752 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3494 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 2 Chain: "B" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2536 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 307} Chain: "C" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2378 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Time building chain proxies: 2.81, per 1000 atoms: 0.26 Number of scatterers: 10752 At special positions: 0 Unit cell: (128.266, 110.874, 106.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2020 8.00 N 1837 7.00 C 6851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 446.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 32.8% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.048A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.522A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.738A pdb=" N GLN A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.604A pdb=" N LYS A 356 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.705A pdb=" N ALA B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.668A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 removed outlier: 3.679A pdb=" N ASP B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.634A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.834A pdb=" N ASN B 253 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.629A pdb=" N TYR B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 315 through 325 removed outlier: 3.875A pdb=" N GLN B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.590A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.562A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.519A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.601A pdb=" N LYS C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 132 removed outlier: 3.754A pdb=" N GLU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.710A pdb=" N LEU C 144 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.731A pdb=" N LEU C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 241 removed outlier: 4.234A pdb=" N LEU C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.530A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.424A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 314 through 326 removed outlier: 3.824A pdb=" N TYR C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 removed outlier: 3.663A pdb=" N SER D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 37 removed outlier: 5.011A pdb=" N VAL A 31 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL A 112 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY A 33 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLN A 114 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 35 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP A 116 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A 37 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 85 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 131 removed outlier: 3.631A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.304A pdb=" N TYR B 60 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 116 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU B 62 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.578A pdb=" N THR B 45 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 47 removed outlier: 6.111A pdb=" N VAL C 6 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 93 removed outlier: 6.483A pdb=" N PHE D 98 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3491 1.34 - 1.46: 2117 1.46 - 1.58: 5291 1.58 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 10964 Sorted by residual: bond pdb=" C ARG C 305 " pdb=" N ASP C 306 " ideal model delta sigma weight residual 1.325 1.288 0.038 1.77e-02 3.19e+03 4.53e+00 bond pdb=" CG LEU C 115 " pdb=" CD2 LEU C 115 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" C ILE B 154 " pdb=" O ILE B 154 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.27e+00 bond pdb=" CB PRO B 129 " pdb=" CG PRO B 129 " ideal model delta sigma weight residual 1.506 1.462 0.044 3.90e-02 6.57e+02 1.26e+00 bond pdb=" CB ASP C 119 " pdb=" CG ASP C 119 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.19e+00 ... (remaining 10959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 14489 1.87 - 3.74: 287 3.74 - 5.60: 34 5.60 - 7.47: 4 7.47 - 9.34: 3 Bond angle restraints: 14817 Sorted by residual: angle pdb=" N LEU C 60 " pdb=" CA LEU C 60 " pdb=" C LEU C 60 " ideal model delta sigma weight residual 109.81 118.43 -8.62 2.21e+00 2.05e-01 1.52e+01 angle pdb=" C LEU A 278 " pdb=" N GLY A 279 " pdb=" CA GLY A 279 " ideal model delta sigma weight residual 121.27 117.07 4.20 1.32e+00 5.74e-01 1.01e+01 angle pdb=" C ASP A 53 " pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 122.56 117.79 4.77 1.50e+00 4.44e-01 1.01e+01 angle pdb=" N ILE B 37 " pdb=" CA ILE B 37 " pdb=" C ILE B 37 " ideal model delta sigma weight residual 112.80 109.23 3.57 1.15e+00 7.56e-01 9.65e+00 angle pdb=" C LEU A 242 " pdb=" N GLU A 243 " pdb=" CA GLU A 243 " ideal model delta sigma weight residual 122.59 118.06 4.53 1.57e+00 4.06e-01 8.34e+00 ... (remaining 14812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6215 17.23 - 34.46: 265 34.46 - 51.69: 64 51.69 - 68.91: 19 68.91 - 86.14: 12 Dihedral angle restraints: 6575 sinusoidal: 2645 harmonic: 3930 Sorted by residual: dihedral pdb=" CA THR A 54 " pdb=" C THR A 54 " pdb=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TRP A 197 " pdb=" C TRP A 197 " pdb=" N ASN A 198 " pdb=" CA ASN A 198 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASN D 95 " pdb=" C ASN D 95 " pdb=" N PRO D 96 " pdb=" CA PRO D 96 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1310 0.050 - 0.099: 308 0.099 - 0.149: 55 0.149 - 0.198: 0 0.198 - 0.248: 2 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CA LEU C 60 " pdb=" N LEU C 60 " pdb=" C LEU C 60 " pdb=" CB LEU C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE C 173 " pdb=" CA ILE C 173 " pdb=" CG1 ILE C 173 " pdb=" CG2 ILE C 173 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1672 not shown) Planarity restraints: 1889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 206 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO D 207 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO C 61 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 265 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO C 266 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 266 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 266 " -0.018 5.00e-02 4.00e+02 ... (remaining 1886 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 657 2.74 - 3.28: 10088 3.28 - 3.82: 16311 3.82 - 4.36: 19684 4.36 - 4.90: 35810 Nonbonded interactions: 82550 Sorted by model distance: nonbonded pdb=" OD1 ASN D 179 " pdb=" OG SER D 200 " model vdw 2.195 3.040 nonbonded pdb=" OG SER D 93 " pdb=" O PRO D 96 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN A 114 " pdb=" OD1 ASP A 116 " model vdw 2.221 3.120 nonbonded pdb=" OG SER C 49 " pdb=" OD1 ASN C 51 " model vdw 2.238 3.040 ... (remaining 82545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10964 Z= 0.175 Angle : 0.651 9.340 14817 Z= 0.372 Chirality : 0.042 0.248 1675 Planarity : 0.004 0.039 1889 Dihedral : 11.775 86.143 4035 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.23), residues: 1336 helix: -0.35 (0.27), residues: 392 sheet: 0.31 (0.23), residues: 445 loop : -0.78 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.012 0.001 TYR B 164 PHE 0.020 0.001 PHE A 237 TRP 0.020 0.002 TRP A 301 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00385 (10964) covalent geometry : angle 0.65069 (14817) hydrogen bonds : bond 0.15053 ( 564) hydrogen bonds : angle 5.75204 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.443 Fit side-chains REVERT: A 55 ILE cc_start: 0.7943 (tp) cc_final: 0.7650 (tp) REVERT: A 69 ASP cc_start: 0.8613 (t0) cc_final: 0.8411 (t0) REVERT: A 161 GLU cc_start: 0.8389 (tt0) cc_final: 0.7830 (tt0) REVERT: B 241 MET cc_start: 0.8669 (mtm) cc_final: 0.8415 (mtp) REVERT: C 111 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7467 (tp30) REVERT: D 176 PHE cc_start: 0.8232 (p90) cc_final: 0.7853 (p90) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1226 time to fit residues: 18.7570 Evaluate side-chains 76 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 424 ASN B 38 GLN B 249 HIS C 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089449 restraints weight = 15173.087| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.73 r_work: 0.2991 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10964 Z= 0.296 Angle : 0.688 11.318 14817 Z= 0.356 Chirality : 0.047 0.288 1675 Planarity : 0.004 0.042 1889 Dihedral : 4.775 22.948 1440 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.58 % Allowed : 4.73 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.23), residues: 1336 helix: 0.04 (0.27), residues: 390 sheet: 0.34 (0.23), residues: 445 loop : -1.09 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 40 TYR 0.022 0.002 TYR B 164 PHE 0.021 0.002 PHE C 145 TRP 0.022 0.002 TRP A 301 HIS 0.007 0.002 HIS C 7 Details of bonding type rmsd covalent geometry : bond 0.00731 (10964) covalent geometry : angle 0.68844 (14817) hydrogen bonds : bond 0.04610 ( 564) hydrogen bonds : angle 4.87361 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.447 Fit side-chains REVERT: A 69 ASP cc_start: 0.8709 (t0) cc_final: 0.8484 (t0) REVERT: A 161 GLU cc_start: 0.8719 (tt0) cc_final: 0.8236 (tt0) REVERT: A 452 MET cc_start: 0.8999 (tpp) cc_final: 0.8772 (tpp) REVERT: B 148 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7920 (mm-30) REVERT: B 241 MET cc_start: 0.8866 (mtm) cc_final: 0.8653 (mtp) REVERT: C 111 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8172 (tp30) REVERT: C 310 ARG cc_start: 0.7583 (mtt180) cc_final: 0.6854 (mmt180) REVERT: D 164 MET cc_start: 0.6880 (tmm) cc_final: 0.6538 (tmm) REVERT: D 176 PHE cc_start: 0.8390 (p90) cc_final: 0.8090 (p90) REVERT: D 178 VAL cc_start: 0.8457 (t) cc_final: 0.8235 (m) outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1164 time to fit residues: 13.9950 Evaluate side-chains 81 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 11 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 124 optimal weight: 30.0000 chunk 128 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 113 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 415 ASN B 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.165966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.092401 restraints weight = 15152.616| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.80 r_work: 0.3039 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10964 Z= 0.132 Angle : 0.534 8.584 14817 Z= 0.279 Chirality : 0.041 0.192 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.330 21.462 1440 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.16 % Allowed : 5.40 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.23), residues: 1336 helix: 0.57 (0.27), residues: 388 sheet: 0.42 (0.23), residues: 440 loop : -1.05 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 228 TYR 0.013 0.001 TYR B 164 PHE 0.014 0.001 PHE B 68 TRP 0.020 0.001 TRP A 301 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00318 (10964) covalent geometry : angle 0.53374 (14817) hydrogen bonds : bond 0.03489 ( 564) hydrogen bonds : angle 4.52363 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.429 Fit side-chains REVERT: A 41 HIS cc_start: 0.8770 (p-80) cc_final: 0.8523 (p90) REVERT: A 69 ASP cc_start: 0.8710 (t0) cc_final: 0.8447 (t0) REVERT: A 161 GLU cc_start: 0.8543 (tt0) cc_final: 0.7913 (tt0) REVERT: B 148 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 241 MET cc_start: 0.8741 (mtm) cc_final: 0.8348 (mtp) REVERT: B 246 HIS cc_start: 0.6700 (m-70) cc_final: 0.6452 (m-70) REVERT: B 250 ASN cc_start: 0.8808 (m-40) cc_final: 0.8583 (m110) REVERT: C 111 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7639 (tp30) REVERT: C 310 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6980 (mmt180) REVERT: D 164 MET cc_start: 0.6898 (tmm) cc_final: 0.6506 (tmm) REVERT: D 176 PHE cc_start: 0.8380 (p90) cc_final: 0.8064 (p90) REVERT: D 178 VAL cc_start: 0.8410 (t) cc_final: 0.8177 (m) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.1249 time to fit residues: 16.2812 Evaluate side-chains 85 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 114 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.164489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092515 restraints weight = 15148.361| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.81 r_work: 0.3047 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10964 Z= 0.128 Angle : 0.515 7.536 14817 Z= 0.270 Chirality : 0.041 0.175 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.178 20.836 1440 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.41 % Allowed : 6.64 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.23), residues: 1336 helix: 0.83 (0.28), residues: 387 sheet: 0.49 (0.23), residues: 437 loop : -0.92 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 228 TYR 0.013 0.001 TYR B 164 PHE 0.025 0.001 PHE C 151 TRP 0.018 0.001 TRP A 301 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00308 (10964) covalent geometry : angle 0.51502 (14817) hydrogen bonds : bond 0.03336 ( 564) hydrogen bonds : angle 4.38565 ( 1602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8707 (t0) cc_final: 0.8414 (t0) REVERT: A 88 PHE cc_start: 0.5118 (OUTLIER) cc_final: 0.4577 (m-80) REVERT: A 161 GLU cc_start: 0.8560 (tt0) cc_final: 0.7908 (tt0) REVERT: A 452 MET cc_start: 0.8844 (tpp) cc_final: 0.8624 (tpp) REVERT: B 148 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 218 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8024 (tptm) REVERT: B 241 MET cc_start: 0.8773 (mtm) cc_final: 0.8343 (mtp) REVERT: B 246 HIS cc_start: 0.6764 (m-70) cc_final: 0.6502 (m-70) REVERT: B 250 ASN cc_start: 0.8800 (m-40) cc_final: 0.8570 (m110) REVERT: C 111 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7609 (tp30) REVERT: C 300 ASN cc_start: 0.7278 (m-40) cc_final: 0.7050 (p0) REVERT: C 310 ARG cc_start: 0.7616 (mtt180) cc_final: 0.7096 (mmt180) REVERT: D 164 MET cc_start: 0.6984 (tmm) cc_final: 0.6627 (tmm) REVERT: D 176 PHE cc_start: 0.8370 (p90) cc_final: 0.8044 (p90) REVERT: D 178 VAL cc_start: 0.8401 (t) cc_final: 0.8168 (m) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.1266 time to fit residues: 17.1312 Evaluate side-chains 92 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 124 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.164369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090651 restraints weight = 15214.477| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.78 r_work: 0.3014 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10964 Z= 0.191 Angle : 0.560 7.257 14817 Z= 0.293 Chirality : 0.043 0.196 1675 Planarity : 0.003 0.043 1889 Dihedral : 4.365 21.907 1440 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.66 % Allowed : 6.64 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.23), residues: 1336 helix: 0.72 (0.27), residues: 389 sheet: 0.54 (0.24), residues: 442 loop : -0.98 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 228 TYR 0.020 0.001 TYR C 320 PHE 0.016 0.001 PHE A 237 TRP 0.019 0.002 TRP A 301 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00471 (10964) covalent geometry : angle 0.56015 (14817) hydrogen bonds : bond 0.03770 ( 564) hydrogen bonds : angle 4.44491 ( 1602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8710 (t0) cc_final: 0.8443 (t0) REVERT: A 88 PHE cc_start: 0.5068 (OUTLIER) cc_final: 0.4543 (m-80) REVERT: A 161 GLU cc_start: 0.8582 (tt0) cc_final: 0.7981 (tt0) REVERT: A 452 MET cc_start: 0.8856 (tpp) cc_final: 0.8610 (tpp) REVERT: B 148 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 246 HIS cc_start: 0.6739 (m-70) cc_final: 0.6475 (m-70) REVERT: B 250 ASN cc_start: 0.8750 (m-40) cc_final: 0.8470 (m110) REVERT: C 36 GLU cc_start: 0.8715 (pt0) cc_final: 0.8445 (pt0) REVERT: C 111 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8030 (tp30) REVERT: C 139 GLU cc_start: 0.7561 (pp20) cc_final: 0.7231 (pp20) REVERT: C 310 ARG cc_start: 0.7397 (mtt180) cc_final: 0.7011 (mmt180) REVERT: D 164 MET cc_start: 0.6968 (tmm) cc_final: 0.6764 (tmm) REVERT: D 176 PHE cc_start: 0.8354 (p90) cc_final: 0.8019 (p90) REVERT: D 178 VAL cc_start: 0.8406 (t) cc_final: 0.8172 (m) outliers start: 20 outliers final: 15 residues processed: 106 average time/residue: 0.1214 time to fit residues: 18.1399 Evaluate side-chains 94 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.164140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092322 restraints weight = 15224.062| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.81 r_work: 0.3038 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10964 Z= 0.121 Angle : 0.514 7.401 14817 Z= 0.270 Chirality : 0.041 0.205 1675 Planarity : 0.003 0.043 1889 Dihedral : 4.124 20.779 1440 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.91 % Allowed : 6.89 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.23), residues: 1336 helix: 0.98 (0.28), residues: 388 sheet: 0.57 (0.24), residues: 437 loop : -0.90 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 228 TYR 0.016 0.001 TYR C 320 PHE 0.024 0.001 PHE C 151 TRP 0.018 0.001 TRP A 301 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00290 (10964) covalent geometry : angle 0.51434 (14817) hydrogen bonds : bond 0.03220 ( 564) hydrogen bonds : angle 4.29197 ( 1602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8726 (t0) cc_final: 0.8417 (t0) REVERT: A 88 PHE cc_start: 0.5207 (OUTLIER) cc_final: 0.4686 (m-80) REVERT: A 161 GLU cc_start: 0.8534 (tt0) cc_final: 0.7890 (tt0) REVERT: A 452 MET cc_start: 0.8822 (tpp) cc_final: 0.8573 (tpp) REVERT: B 148 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 241 MET cc_start: 0.8704 (mtm) cc_final: 0.8182 (mtp) REVERT: B 246 HIS cc_start: 0.6736 (m-70) cc_final: 0.6471 (m-70) REVERT: B 250 ASN cc_start: 0.8754 (m-40) cc_final: 0.8512 (m110) REVERT: C 111 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7653 (tp30) REVERT: C 300 ASN cc_start: 0.7218 (m-40) cc_final: 0.6914 (p0) REVERT: C 305 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7727 (ttp80) REVERT: C 310 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6980 (mmt180) REVERT: D 164 MET cc_start: 0.7012 (tmm) cc_final: 0.6780 (tmm) REVERT: D 176 PHE cc_start: 0.8340 (p90) cc_final: 0.8010 (p90) REVERT: D 178 VAL cc_start: 0.8393 (t) cc_final: 0.8168 (m) outliers start: 23 outliers final: 16 residues processed: 102 average time/residue: 0.1227 time to fit residues: 17.4722 Evaluate side-chains 98 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 132 optimal weight: 0.1980 chunk 126 optimal weight: 30.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090581 restraints weight = 15226.942| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.81 r_work: 0.3021 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10964 Z= 0.171 Angle : 0.546 7.325 14817 Z= 0.286 Chirality : 0.042 0.213 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.246 21.486 1440 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.74 % Allowed : 7.06 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.23), residues: 1336 helix: 0.80 (0.27), residues: 394 sheet: 0.57 (0.24), residues: 442 loop : -0.91 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 228 TYR 0.017 0.001 TYR C 320 PHE 0.017 0.001 PHE A 123 TRP 0.018 0.001 TRP A 301 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00420 (10964) covalent geometry : angle 0.54566 (14817) hydrogen bonds : bond 0.03604 ( 564) hydrogen bonds : angle 4.34708 ( 1602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8714 (t0) cc_final: 0.8445 (t0) REVERT: A 88 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4535 (m-80) REVERT: A 161 GLU cc_start: 0.8591 (tt0) cc_final: 0.7996 (tt0) REVERT: A 164 ARG cc_start: 0.7695 (ptp90) cc_final: 0.7402 (ptp90) REVERT: A 452 MET cc_start: 0.8864 (tpp) cc_final: 0.8598 (tpp) REVERT: B 136 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8435 (mmmt) REVERT: B 148 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 246 HIS cc_start: 0.6703 (m-70) cc_final: 0.6440 (m-70) REVERT: B 250 ASN cc_start: 0.8766 (m-40) cc_final: 0.8495 (m110) REVERT: C 111 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7701 (tp30) REVERT: C 151 PHE cc_start: 0.8382 (t80) cc_final: 0.8082 (t80) REVERT: C 154 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: C 173 ILE cc_start: 0.8548 (mp) cc_final: 0.8217 (mm) REVERT: C 305 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7735 (ttp80) REVERT: C 310 ARG cc_start: 0.7383 (mtt180) cc_final: 0.7008 (mmt180) REVERT: D 164 MET cc_start: 0.6964 (tmm) cc_final: 0.6710 (tmm) REVERT: D 176 PHE cc_start: 0.8342 (p90) cc_final: 0.7997 (p90) REVERT: D 178 VAL cc_start: 0.8431 (t) cc_final: 0.8194 (m) outliers start: 21 outliers final: 13 residues processed: 100 average time/residue: 0.1187 time to fit residues: 16.7060 Evaluate side-chains 96 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 126 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.0020 chunk 30 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 overall best weight: 0.9668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.164122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092695 restraints weight = 15106.924| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.73 r_work: 0.3047 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10964 Z= 0.123 Angle : 0.513 8.447 14817 Z= 0.268 Chirality : 0.041 0.223 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.081 20.855 1440 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.66 % Allowed : 7.56 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.23), residues: 1336 helix: 0.98 (0.28), residues: 394 sheet: 0.59 (0.24), residues: 437 loop : -0.90 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 228 TYR 0.015 0.001 TYR C 320 PHE 0.018 0.001 PHE A 123 TRP 0.019 0.001 TRP A 301 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00297 (10964) covalent geometry : angle 0.51349 (14817) hydrogen bonds : bond 0.03189 ( 564) hydrogen bonds : angle 4.24825 ( 1602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8704 (t0) cc_final: 0.8442 (t0) REVERT: A 88 PHE cc_start: 0.4994 (OUTLIER) cc_final: 0.4569 (m-80) REVERT: A 161 GLU cc_start: 0.8569 (tt0) cc_final: 0.7939 (tt0) REVERT: A 164 ARG cc_start: 0.7757 (ptp90) cc_final: 0.7533 (ptp90) REVERT: A 452 MET cc_start: 0.8857 (tpp) cc_final: 0.8585 (tpp) REVERT: B 136 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8347 (mmmt) REVERT: B 148 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 246 HIS cc_start: 0.6781 (m-70) cc_final: 0.6532 (m-70) REVERT: B 250 ASN cc_start: 0.8781 (m-40) cc_final: 0.8528 (m110) REVERT: C 111 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7693 (tp30) REVERT: C 151 PHE cc_start: 0.8266 (t80) cc_final: 0.8032 (t80) REVERT: C 154 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: C 173 ILE cc_start: 0.8489 (mp) cc_final: 0.8205 (mm) REVERT: C 305 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7951 (ttp80) REVERT: C 310 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7078 (mmt180) REVERT: D 164 MET cc_start: 0.6982 (tmm) cc_final: 0.6737 (tmm) REVERT: D 176 PHE cc_start: 0.8315 (p90) cc_final: 0.7959 (p90) REVERT: D 178 VAL cc_start: 0.8385 (t) cc_final: 0.8167 (m) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.1132 time to fit residues: 16.1925 Evaluate side-chains 100 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 65 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 104 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.165947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093078 restraints weight = 15054.843| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.75 r_work: 0.3047 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10964 Z= 0.122 Angle : 0.509 6.614 14817 Z= 0.267 Chirality : 0.041 0.242 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.038 20.466 1440 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.41 % Allowed : 7.81 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.23), residues: 1336 helix: 1.11 (0.28), residues: 390 sheet: 0.60 (0.24), residues: 437 loop : -0.88 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 228 TYR 0.015 0.001 TYR C 320 PHE 0.018 0.001 PHE A 123 TRP 0.018 0.001 TRP A 301 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00293 (10964) covalent geometry : angle 0.50861 (14817) hydrogen bonds : bond 0.03192 ( 564) hydrogen bonds : angle 4.21028 ( 1602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8700 (t0) cc_final: 0.8438 (t0) REVERT: A 88 PHE cc_start: 0.5193 (OUTLIER) cc_final: 0.4768 (m-80) REVERT: A 161 GLU cc_start: 0.8563 (tt0) cc_final: 0.8264 (tt0) REVERT: A 164 ARG cc_start: 0.7674 (ptp90) cc_final: 0.7470 (ptp90) REVERT: A 452 MET cc_start: 0.8816 (tpp) cc_final: 0.8549 (tpp) REVERT: B 136 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8341 (mmmt) REVERT: B 148 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7812 (mm-30) REVERT: B 246 HIS cc_start: 0.6756 (m-70) cc_final: 0.6502 (m-70) REVERT: B 250 ASN cc_start: 0.8769 (m-40) cc_final: 0.8517 (m110) REVERT: C 111 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7650 (tp30) REVERT: C 151 PHE cc_start: 0.8190 (t80) cc_final: 0.7981 (t80) REVERT: C 154 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: C 300 ASN cc_start: 0.7292 (m-40) cc_final: 0.6925 (p0) REVERT: C 305 ARG cc_start: 0.8258 (ttp80) cc_final: 0.8030 (ttp80) REVERT: D 164 MET cc_start: 0.6951 (tmm) cc_final: 0.6697 (tmm) REVERT: D 176 PHE cc_start: 0.8278 (p90) cc_final: 0.7905 (p90) REVERT: D 178 VAL cc_start: 0.8383 (t) cc_final: 0.8166 (m) outliers start: 17 outliers final: 14 residues processed: 95 average time/residue: 0.1055 time to fit residues: 14.1503 Evaluate side-chains 95 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.166209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094372 restraints weight = 15246.153| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.67 r_work: 0.3089 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10964 Z= 0.129 Angle : 0.517 6.664 14817 Z= 0.271 Chirality : 0.041 0.244 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.043 20.730 1440 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.50 % Allowed : 8.06 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.23), residues: 1336 helix: 1.14 (0.28), residues: 390 sheet: 0.60 (0.24), residues: 437 loop : -0.90 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 228 TYR 0.014 0.001 TYR C 320 PHE 0.019 0.001 PHE A 123 TRP 0.018 0.001 TRP A 301 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00313 (10964) covalent geometry : angle 0.51665 (14817) hydrogen bonds : bond 0.03244 ( 564) hydrogen bonds : angle 4.19990 ( 1602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8729 (t0) cc_final: 0.8456 (t0) REVERT: A 88 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4818 (m-80) REVERT: A 161 GLU cc_start: 0.8730 (tt0) cc_final: 0.8484 (tt0) REVERT: A 452 MET cc_start: 0.8899 (tpp) cc_final: 0.8640 (tpp) REVERT: B 60 TYR cc_start: 0.8703 (p90) cc_final: 0.8406 (p90) REVERT: B 136 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8425 (mmmt) REVERT: B 246 HIS cc_start: 0.6766 (m-70) cc_final: 0.6505 (m-70) REVERT: B 250 ASN cc_start: 0.8865 (m-40) cc_final: 0.8619 (m110) REVERT: C 111 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8122 (tp30) REVERT: C 151 PHE cc_start: 0.8210 (t80) cc_final: 0.7985 (t80) REVERT: C 154 TRP cc_start: 0.8289 (OUTLIER) cc_final: 0.7821 (m-10) REVERT: D 164 MET cc_start: 0.6967 (tmm) cc_final: 0.6720 (tmm) REVERT: D 176 PHE cc_start: 0.8255 (p90) cc_final: 0.7873 (p90) REVERT: D 178 VAL cc_start: 0.8374 (t) cc_final: 0.8164 (m) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.1090 time to fit residues: 15.0547 Evaluate side-chains 94 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089580 restraints weight = 15178.032| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.77 r_work: 0.3003 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10964 Z= 0.226 Angle : 0.592 7.246 14817 Z= 0.309 Chirality : 0.044 0.241 1675 Planarity : 0.004 0.042 1889 Dihedral : 4.356 21.713 1440 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.25 % Allowed : 8.55 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.23), residues: 1336 helix: 0.86 (0.27), residues: 391 sheet: 0.64 (0.24), residues: 435 loop : -1.00 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 228 TYR 0.021 0.002 TYR B 164 PHE 0.019 0.002 PHE A 123 TRP 0.017 0.002 TRP A 301 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00556 (10964) covalent geometry : angle 0.59155 (14817) hydrogen bonds : bond 0.03919 ( 564) hydrogen bonds : angle 4.39874 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3502.78 seconds wall clock time: 60 minutes 33.85 seconds (3633.85 seconds total)